Beta diversity

From 16S rRNA-gene sequencing of cow RUMEN microbiome samples: - 6 treatments for rumen samples + ruminal liquid (base) + (“AE1”,“AE sintético 1”,“Carvacrol”, “p-cymene”, “γ-terpinene”, “no treatment (ruminal liquid + diet)”)

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

## Warning in as.dist.default(matx): non-square matrix
## Warning in x[row(x) > col(x)] <- d^2: number of items to replace is not a
## multiple of replacement length

Clustering by treatment (PCA): after removing samples from treatment no treatment (ruminal liquid + diet) # BECAUSE WE KNOW THAT THERE WE SHOULD NOT HAVE DIFFERENCES BETWEEN GROUPS

MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

## Warning in metaMDS(matx0, k = 3): stress is (nearly) zero: you may have
## insufficient data

Clustering by type (MDS): NMDS2 vs NMDS3

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

Below the ANOVA table from the model:

\[ X = \mu + treatment + + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 6 0.1670642 0.027844 1.361631 0.1536547 0.203
residuals 45 0.9202063 0.020449 NA 0.8463453 NA
total 51 1.0872705 NA NA 1.0000000 NA

going 3D

## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.005866665 
## Run 1 stress 0.002880717 
## ... New best solution
## ... Procrustes: rmse 0.04570152  max resid 0.1011523 
## Run 2 stress 0.002993376 
## ... Procrustes: rmse 0.01197886  max resid 0.0252612 
## Run 3 stress 0.004457099 
## Run 4 stress 0.008358046 
## Run 5 stress 0.002991392 
## ... Procrustes: rmse 0.02118136  max resid 0.04484306 
## Run 6 stress 0.004604658 
## Run 7 stress 0.002968823 
## ... Procrustes: rmse 0.02073788  max resid 0.04566674 
## Run 8 stress 0.002156464 
## ... New best solution
## ... Procrustes: rmse 0.01458369  max resid 0.0336482 
## Run 9 stress 0.006683282 
## Run 10 stress 0.001652964 
## ... New best solution
## ... Procrustes: rmse 0.01260981  max resid 0.02825254 
## Run 11 stress 0.0007457592 
## ... New best solution
## ... Procrustes: rmse 0.006741449  max resid 0.01520747 
## Run 12 stress 0.008546079 
## Run 13 stress 0.008932748 
## Run 14 stress 0.002043376 
## Run 15 stress 0.0005669045 
## ... New best solution
## ... Procrustes: rmse 0.00227706  max resid 0.004998075 
## ... Similar to previous best
## Run 16 stress 0.001146092 
## Run 17 stress 0.001468972 
## Run 18 stress 0.001723621 
## Run 19 stress 0.0002764154 
## ... New best solution
## ... Procrustes: rmse 0.003813089  max resid 0.008499326 
## ... Similar to previous best
## Run 20 stress 0.006475395 
## *** Solution reached

AE1

AE sintético 1

Carvacrol

p-cymene

γ-terpinene

no treatment (ruminal liquid + diet)